Sure! You'll just be looking at correlations between secondary structure elements, disregarding the role that the loops may play. But it's a sound approach.
:) Tsjerk On Tue, Nov 1, 2011 at 3:44 PM, vivek modi <[email protected]> wrote: > Hi, > > I plan to perform PCA on a globular protein which I am studying. The > simulation for the same is done for 100ns. > I have small doubt. Is it appropriate to perform PCA to study the movement > in protein on only secondary structure elements (helices in this case). > My protein contains long loops which do not play any role. Is it appropriate > to group only the helices together ignoring the loops and perform PCA ? > > Any help is appreciated. > > > Regards, > > -Vivek Modi > Graduate Student > IITK. > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
